BtaINT0122352 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006828 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chr5:32714229-32714656:+
Coord C1 exon
chr5:32714229-32714354
Coord A exon
chr5:32714355-32714474
Coord C2 exon
chr5:32714475-32714656
Length
120 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCTG
5' ss Score
4.87
3' ss Seq
CAGTGCTGCCCCCTGCCCAGGTG
3' ss Score
5.34
Exon sequences
Seq C1 exon
ACCCCACACCCCGATCAGCTGGGGCCCACTGTGGGCTCTGCCGAGGGGCTGGACCTGGTGAGCACCAAGGACCTGGCGGGCCAGCTCACGGACCACGACTGGAGCCTCTTCAACAGCATCCACCAG
Seq A exon
GTGCTGGGGTGGAGCGGAGGGGAGGAGAGTGGGCGATGGGGATGCCCTGCCCCACGCGCAGCCTCGTGTGCTGGACGCCCTGCCCTGCGTGCTGACCTCGCAGTGCTGCCCCCTGCCCAG
Seq C2 exon
GTGGAGCTGATCCACTATGTGCTGGGCCCCCAGCACCTGCGGGACGTCACCACCGCCAACCTGGAGCGCTTCATGCGCCGCTTCAACGAGCTGCAGTACTGGGTGGCCACGGAGCTGTGTCTCTGCTCTGTGCCCGGCCTACGGGCCCAGCTGCTCAGGAAGTTCATCAAACTGGCAGCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006828:ENSBTAT00000008976:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.262 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PU(12.9=57.1)
A:
NA
C2:
PF0061714=RasGEF=FE(32.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGAGCACCAAGGACCTGG
R:
TGGGCTGCCAGTTTGATGAAC
Band lengths:
251-371
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]